This issue is a simple one to explain.
3dmark2001SE works primarily on CPU speed with graphics being tested 2nd to the CPU. If you want a combined score then this is the benchmark for you - Sli users be warned, you will be CPU limited in this test, do not expect to double your score on this test - the CPU can't keep up (unless you have FX-53/55 of course)
The scores you are posting for 3dm03 and 3dm05 reflect 'true' graphics performance on the given feature (bump mapping, AA, AF etc). Therefore unless you have a really old system the scores that you achieve with your 6800GT should be similar to other systems with a 6800GT.
The small differences can be related to memory timings, overclock settings and how much junk you have on your system.
Hope this helps.
Cheers
Mav